Structure of PDB 1gz4 Chain A Binding Site BS01

Receptor Information
>1gz4 Chain A (length=551) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHRNL
KKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLACSQ
YGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDL
GVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMGLY
QKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREK
YCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANL
IVMSMVENGLSEQEAQKKIWMFDKYGLLVKGRKAKIDSYQEPFTHSAPES
IPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFALSNP
TAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFP
GVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEV
SINIAIKVTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEW
P
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain1gz4 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1gz4 Molecular Mechanism for the Regulation of Human Mitochondrial Nad(P)(+)-Dependent Malic Enzyme by ATP and Fumarate
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R165 N259 G311 A312 G313 E314 A315 D345 K346 V392 A393
Binding residue
(residue number reindexed from 1)		R143 N237 G289 A290 G291 E292 A293 D323 K324 V370 A371
Annotation score3
Binding affinityMOAD: Ki=0.2mM
PDBbind-CN: -logKd/Ki=3.70,Ki=0.2mM
Enzymatic activity
Catalytic site (original residue number in PDB) Y112 R165 K183 E255 D256 D278 D279 N421
Catalytic site (residue number reindexed from 1) Y90 R143 K161 E233 D234 D256 D257 N399
Enzyme Commision number 1.1.1.38: malate dehydrogenase (oxaloacetate-decarboxylating).
Gene Ontology
Molecular Function
GO:0004470 malic enzyme activity
GO:0004471 malate dehydrogenase (decarboxylating) (NAD+) activity
GO:0004473 malate dehydrogenase (decarboxylating) (NADP+) activity
GO:0008948 oxaloacetate decarboxylase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0046872 metal ion binding
GO:0051287 NAD binding
Biological Process
GO:0006090 pyruvate metabolic process
GO:0006108 malate metabolic process
GO:1902031 regulation of NADP metabolic process
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1gz4, PDBe:1gz4, PDBj:1gz4
PDBsum1gz4
PubMed12121650
UniProtP23368|MAOM_HUMAN NAD-dependent malic enzyme, mitochondrial (Gene Name=ME2)

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